A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

G Xue, X Zhang, W Li, L Zhang, Z Zhang, X Zhou… - Elife, 2024 - elifesciences.org
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory
mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding …

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

F Wu, RQ Su, YC Lai, X Wang - Elife, 2017 - elifesciences.org
The process of cell fate determination has been depicted intuitively as cells travelling and
resting on a rugged landscape, which has been probed by various theoretical studies …

[PDF][PDF] Characterization of cell-fate decision landscapes by estimating transcription factor dynamics

S Jiménez, V Schreiber, R Mercier, G Gradwohl… - Cell Reports …, 2023 - cell.com
Time-specific modulation of gene expression during differentiation by transcription factors
promotes cell diversity. However, estimating their dynamic regulatory activity at the single …

Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation

B Huang, M Lu, M Galbraith… - Journal of The …, 2020 - royalsocietypublishing.org
Stem cells can precisely and robustly undergo cellular differentiation and lineage
commitment, referred to as stemness. However, how the gene network underlying stemness …

ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination

Q Xu, G Georgiou, S Frölich… - Nucleic acids …, 2021 - academic.oup.com
Proper cell fate determination is largely orchestrated by complex gene regulatory networks
centered around transcription factors. However, experimental elucidation of key transcription …

A meta-analysis of Boolean network models reveals design principles of gene regulatory networks

C Kadelka, TM Butrie, E Hilton, J Kinseth, A Schmidt… - Science …, 2024 - science.org
Gene regulatory networks (GRNs) play a central role in cellular decision-making.
Understanding their structure and how it impacts their dynamics constitutes thus a …

Engineering of regulated stochastic cell fate determination

M Wu, RQ Su, X Li, T Ellis, YC Lai… - Proceedings of the …, 2013 - National Acad Sciences
Both microbes and multicellular organisms actively regulate their cell fate determination to
cope with changing environments or to ensure proper development. Here, we use synthetic …

A neural network-based model framework for cell-fate decisions and development

M Paczkó, D Vörös, P Szabó, G Jékely… - Communications …, 2024 - nature.com
Gene regulatory networks (GRNs) fulfill the essential function of maintaining the stability of
cellular differentiation states by sustaining lineage-specific gene expression, while driving …

A deterministic map of Waddington's epigenetic landscape for cell fate specification

S Bhattacharya, Q Zhang, ME Andersen - BMC systems biology, 2011 - Springer
Background The image of the" epigenetic landscape", with a series of branching valleys and
ridges depicting stable cellular states and the barriers between those states, has been a …

Expression pattern determines regulatory logic

C Mora-Martinez - PLoS One, 2021 - journals.plos.org
Large amounts of effort have been invested in trying to understand how a single genome is
able to specify the identity of hundreds of cell types. Inspired by some aspects of …